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- PDB-7k17: Re-refined crystal structure of DNA-dependent protein kinase cata... -

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基本情報

登録情報
データベース: PDB / ID: 7k17
タイトルRe-refined crystal structure of DNA-dependent protein kinase catalytic subunit complexed with Ku80 C-terminal helix
要素
  • DNA-dependent protein kinase catalytic subunit
  • X-ray repair cross-complementing protein 5
キーワードDNA BINDING PROTEIN / NHEJ / V(D)J recombination / DNA repair
機能・相同性
機能・相同性情報


Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / regulation of telomere maintenance / recombinational repair / U3 snoRNA binding / protein localization to chromosome, telomeric region / 2-LTR circle formation / telomeric DNA binding / hematopoietic stem cell proliferation / positive regulation of protein kinase activity / site of DNA damage / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / neurogenesis / telomere maintenance / DNA helicase activity / activation of innate immune response / cellular response to leukemia inhibitory factor / Nonhomologous End-Joining (NHEJ) / small-subunit processome / enzyme activator activity / cellular response to gamma radiation / protein-DNA complex / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / double-strand break repair via nonhomologous end joining / double-strand break repair / double-stranded DNA binding / secretory granule lumen / DNA recombination / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / protein-containing complex binding / nucleolus / protein-containing complex / ATP hydrolysis activity / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol
類似検索 - 分子機能
Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen ...Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
類似検索 - ドメイン・相同性
X-ray repair cross-complementing protein 5
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4.3 Å
データ登録者Chen, X. / Gellert, M. / Yang, W.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) 米国
引用ジャーナル: Science / 年: 2017
タイトル: DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair.
著者: Sibanda, B.L. / Chirgadze, D.Y. / Ascher, D.B. / Blundell, T.L.
履歴
登録2020年9月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年1月6日Provider: repository / タイプ: Initial release
改定 1.12021年1月13日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22021年3月3日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
改定 1.32023年10月18日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 0THIS ENTRY 7K17 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5LUQ, DETERMINED BY B.L. ...THIS ENTRY 7K17 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5LUQ, DETERMINED BY B.L.Sibanda, D.Y.Chirgadze, D.B.Ascher, T.L.Blundell

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: DNA-dependent protein kinase catalytic subunit
B: DNA-dependent protein kinase catalytic subunit
D: X-ray repair cross-complementing protein 5
C: X-ray repair cross-complementing protein 5


分子量 (理論値)分子数
合計 (水以外)947,9414
ポリマ－947,9414
非ポリマー00
水00
1
A: DNA-dependent protein kinase catalytic subunit
C: X-ray repair cross-complementing protein 5


分子量 (理論値)分子数
合計 (水以外)473,9712
ポリマ－473,9712
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-11 kcal/mol
Surface area166350 Å2
手法PISA
2
B: DNA-dependent protein kinase catalytic subunit
D: X-ray repair cross-complementing protein 5


分子量 (理論値)分子数
合計 (水以外)473,9712
ポリマ－473,9712
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-10 kcal/mol
Surface area162840 Å2
手法PISA
単位格子
Length a, b, c (Å)169.120, 132.640, 296.590
Angle α, β, γ (deg.)90.000, 105.530, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA8 - 2358 - 235
121ASPASPTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA241 - 400241 - 400
131VALVALVALVAL(chain 'A' and (resid 8 through 61 or (resid 62...AA407 - 496407 - 496
141VALVALLEULEU(chain 'A' and (resid 8 through 61 or (resid 62...AA521 - 545521 - 545
151ASNASNTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA561 - 587561 - 587
161METMETGLUGLU(chain 'A' and (resid 8 through 61 or (resid 62...AA602 - 684602 - 684
171TYRTYRLYSLYS(chain 'A' and (resid 8 through 61 or (resid 62...AA701 - 801701 - 801
181ILEILEGLNGLN(chain 'A' and (resid 8 through 61 or (resid 62...AA846 - 947846 - 947
191PROPROCYSCYS(chain 'A' and (resid 8 through 61 or (resid 62...AA956 - 1229956 - 1229
1101GLNGLNALAALA(chain 'A' and (resid 8 through 61 or (resid 62...AA1251 - 13021251 - 1302
1111SERSERTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA1323 - 13511323 - 1351
1121LEULEUPROPRO(chain 'A' and (resid 8 through 61 or (resid 62...AA1359 - 14931359 - 1493
1131PROPROVALVAL(chain 'A' and (resid 8 through 61 or (resid 62...AA1501 - 15371501 - 1537
1141GLYGLYSERSER(chain 'A' and (resid 8 through 61 or (resid 62...AA1556 - 16571556 - 1657
1151HISHISVALVAL(chain 'A' and (resid 8 through 61 or (resid 62...AA1665 - 19941665 - 1994
1161SERSERTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA2034 - 20472034 - 2047
1171GLUGLULEULEU(chain 'A' and (resid 8 through 61 or (resid 62...AA2082 - 21082082 - 2108
1181PROPROSERSER(chain 'A' and (resid 8 through 61 or (resid 62...AA2119 - 25932119 - 2593
1191UNKUNKUNKUNK(chain 'A' and (resid 8 through 61 or (resid 62...AA2606 - 26132601 - 2608
1201UNKUNKUNKUNK(chain 'A' and (resid 8 through 61 or (resid 62...AA2739 - 27402610 - 2611
1211UNKUNKUNKUNK(chain 'A' and (resid 8 through 61 or (resid 62...AA2742 - 27642613 - 2635
1221ASPASPASPASP(chain 'A' and (resid 8 through 61 or (resid 62...AA27792637
1231GLNGLNLEULEU(chain 'A' and (resid 8 through 61 or (resid 62...AA2784 - 28972642 - 2755
1241ASPASPTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA2919 - 31982777 - 3056
1251ASPASPLEULEU(chain 'A' and (resid 8 through 61 or (resid 62...AA3226 - 33623084 - 3220
1261ASPASPGLNGLN(chain 'A' and (resid 8 through 61 or (resid 62...AA3369 - 33903227 - 3248
1271ALAALAGLUGLU(chain 'A' and (resid 8 through 61 or (resid 62...AA3406 - 34293264 - 3287
1281GLNGLNMETMET(chain 'A' and (resid 8 through 61 or (resid 62...AA3440 - 41283298 - 3986
211VALVALTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB8 - 2358 - 235
221ASPASPTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB241 - 400241 - 400
231VALVALVALVAL(chain 'B' and (resid 8 through 53 or (resid 54...BB407 - 496407 - 496
241VALVALLEULEU(chain 'B' and (resid 8 through 53 or (resid 54...BB521 - 545521 - 545
251ASNASNTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB561 - 587561 - 587
261METMETGLUGLU(chain 'B' and (resid 8 through 53 or (resid 54...BB602 - 684602 - 684
271TYRTYRLYSLYS(chain 'B' and (resid 8 through 53 or (resid 54...BB701 - 801701 - 801
281ILEILEGLNGLN(chain 'B' and (resid 8 through 53 or (resid 54...BB846 - 947846 - 947
291PROPROCYSCYS(chain 'B' and (resid 8 through 53 or (resid 54...BB956 - 1229956 - 1229
2101GLNGLNALAALA(chain 'B' and (resid 8 through 53 or (resid 54...BB1251 - 13021251 - 1302
2111SERSERTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB1323 - 13511323 - 1351
2121LEULEUPROPRO(chain 'B' and (resid 8 through 53 or (resid 54...BB1359 - 14931359 - 1493
2131PROPROVALVAL(chain 'B' and (resid 8 through 53 or (resid 54...BB1501 - 15371501 - 1537
2141GLYGLYSERSER(chain 'B' and (resid 8 through 53 or (resid 54...BB1556 - 16571556 - 1657
2151HISHISVALVAL(chain 'B' and (resid 8 through 53 or (resid 54...BB1665 - 19941665 - 1994
2161SERSERTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB2034 - 20472034 - 2047
2171GLUGLULEULEU(chain 'B' and (resid 8 through 53 or (resid 54...BB2082 - 21082082 - 2108
2181PROPROSERSER(chain 'B' and (resid 8 through 53 or (resid 54...BB2119 - 25932119 - 2593
2191UNKUNKUNKUNK(chain 'B' and (resid 8 through 53 or (resid 54...BB2603 - 26102599 - 2606
2201UNKUNKUNKUNK(chain 'B' and (resid 8 through 53 or (resid 54...BB2612 - 26132608 - 2609
2211UNKUNKUNKUNK(chain 'B' and (resid 8 through 53 or (resid 54...BB2740 - 27622611 - 2633
2221UNKUNKUNKUNK(chain 'B' and (resid 8 through 53 or (resid 54...BB27642635
2231GLNGLNLEULEU(chain 'B' and (resid 8 through 53 or (resid 54...BB2784 - 28972642 - 2755
2241ASPASPTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB2919 - 31982777 - 3056
2251ASPASPLEULEU(chain 'B' and (resid 8 through 53 or (resid 54...BB3226 - 33623084 - 3220
2261ASPASPGLNGLN(chain 'B' and (resid 8 through 53 or (resid 54...BB3369 - 33903227 - 3248
2271ALAALAGLUGLU(chain 'B' and (resid 8 through 53 or (resid 54...BB3406 - 34293264 - 3287
2281GLNGLNMETMET(chain 'B' and (resid 8 through 53 or (resid 54...BB3440 - 41283298 - 3986
112ASPASPILEILEchain 'C'CD724 - 732184 - 192
212ASPASPILEILEchain 'D'DC724 - 732184 - 192

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 DNA-dependent protein kinase catalytic subunit / DNA-PKcs / DNPK1 / p460


分子量: 452515.625 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: non-specific serine/threonine protein kinase
#2: タンパク質 X-ray repair cross-complementing protein 5 / 86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase ...86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase II 80 kDa subunit / CTC box-binding factor 85 kDa subunit / CTCBF / DNA repair protein XRCC5 / Ku80 / Ku86 / Lupus Ku autoantigen protein p86 / Nuclear factor IV / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)


分子量: 21454.877 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: XRCC5, G22P2 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P13010, 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与
配列の詳細The complete sample sequence of DNA-dependent protein kinase catalytic subunit is ...The complete sample sequence of DNA-dependent protein kinase catalytic subunit is MAGSGAGVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTSLVFS RDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVEIKNTCTSVYTKDRA AKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKFYGELALKKKIPDTVLEKVYELLGL LGEVHPSEMINNAENLFRAFLGELKTQMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEE DPQTSREIFNFVLKAIRPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKW CAHTNVELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSNNKELS IAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDDRVYQMPSFLQSVASV LLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQLVCCRAIVKVFLALAAKGPVLRNCIS TVVHQGLIRICSKPVVLPKGPESESEDHRASGEVRTGKWKVPTYKDYVDLFRHLLSSDQM MDSILADEAFFSVNSSSESLNHLLYDEFVKSVLKIVEKLDLTLEIQTVGEQENGDEAPGV WMIPTSDPAANLHPAKPKDFSAFINLVEFCREILPEKQAEFFEPWVYSFSYELILQSTRL PLISGFYKLLSITVRNAKKIKYFEGVSPKSLKHSPEDPEKYSCFALFVKFGKEVAVKMKQ YKDELLASCLTFLLSLPHNIIELDVRAYVPALQMAFKLGLSYTPLAEVGLNALEEWSIYI DRHVMQPYYKDILPCLDGYLKTSALSDETKNNWEVSALSRAAQKGFNKVVLKHLKKTKNL SSNEAISLEEIRIRVVQMLGSLGGQINKNLLTVTSSDEMMKSYVAWDREKRLSFAVPFRE MKPVIFLDVFLPRVTELALTASDRQTKVAACELLHSMVMFMLGKATQMPEGGQGAPPMYQ LYKRTFPVLLRLACDVDQVTRQLYEPLVMQLIHWFTNNKKFESQDTVALLEAILDGIVDP VDSTLRDFCGRCIREFLKWSIKQITPQQQEKSPVNTKSLFKRLYSLALHPNAFKRLGASL AFNNIYREFREEESLVEQFVFEALVIYMESLALAHADEKSLGTIQQCCDAIDHLCRIIEK KHVSLNKAKKRRLPRGFPPSASLCLLDLVKWLLAHCGRPQTECRHKSIELFYKFVPLLPG NRSPNLWLKDVLKEEGVSFLINTFEGGGCGQPSGILAQPTLLYLRGPFSLQATLCWLDLL LAALECYNTFIGERTVGALQVLGTEAQSSLLKAVAFFLESIAMHDIIAAEKCFGTGAAGN RTSPQEGERYNYSKCTVVVRIMEFTTTLLNTSPEGWKLLKKDLCNTHLMRVLVQTLCEPA SIGFNIGDVQVMAHLPDVCVNLMKALKMSPYKDILETHLREKITAQSIEELCAVNLYGPD AQVDRSRLAAVVSACKQLHRAGLLHNILPSQSTDLHHSVGTELLSLVYKGIAPGDERQCL PSLDLSCKQLASGLLELAFAFGGLCERLVSLLLNPAVLSTASLGSSQGSVIHFSHGEYFY SLFSETINTELLKNLDLAVLELMQSSVDNTKMVSAVLNGMLDQSFRERANQKHQGLKLAT TILQHWKKCDSWWAKDSPLETKMAVLALLAKILQIDSSVSFNTSHGSFPEVFTTYISLLA DTKLDLHLKGQAVTLLPFFTSLTGGSLEELRRVLEQLIVAHFPMQSREFPPGTPRFNNYV DCMKKFLDALELSQSPMLLELMTEVLCREQQHVMEELFQSSFRRIARRGSCVTQVGLLES VYEMFRKDDPRLSFTRQSFVDRSLLTLLWHCSLDALREFFSTIVVDAIDVLKSRFTKLNE STFDTQITKKMGYYKILDVMYSRLPKDDVHAKESKINQVFHGSCITEGNELTKTLIKLCY DAFTENMAGENQLLERRRLYHCAAYNCAISVICCVFNELKFYQGFLFSEKPEKNLLIFEN LIDLKRRYNFPVEVEVPMERKKKYIEIRKEAREAANGDSDGPSYMSSLSYLADSTLSEEM SQFDFSTGVQSYSYSSQDPRPATGRFRRREQRDPTVHDDVLELEMDELNRHECMAPLTAL VKHMHRSLGPPQGEEDSVPRDLPSWMKFLHGKLGNPIVPLNIRLFLAKLVINTEEVFRPY AKHWLSPLLQLAASENNGGEGIHYMVVEIVATILSWTGLATPTGVPKDEVLANRLLNFLM KHVFHPKRAVFRHNLEIIKTLVECWKDCLSIPYRLIFEKFSGKDPNSKDNSVGIQLLGIV MANDLPPYDPQCGIQSSEYFQALVNNMSFVRYKEVYAAAAEVLGLILRYVMERKNILEES LCELVAKQLKQHQNTMEDKFIVCLNKVTKSFPPLADRFMNAVFFLLPKFHGVLKTLCLEV VLCRVEGMTELYFQLKSKDFVQVMRHRDDERQKVCLDIIYKMMPKLKPVELRELLNPVVE FVSHPSTTCREQMYNILMWIHDNYRDPESETDNDSQEIFKLAKDVLIQGLIDENPGLQLI IRNFWSHETRLPSNTLDRLLALNSLYSPKIEVHFLSLATNFLLEMTSMSPDYPNPMFEHP LSECEFQEYTIDSDWRFRSTVLTPMFVETQASQGTLQTRTQEGSLSARWPVAGQIRATQQ QHDFTLTQTADGRSSFDWLTGSSTDPLVDHTSPSSDSLLFAHKRSERLQRAPLKSVGPDF GKKRLGLPGDEVDNKVKGAAGRTDLLRLRRRFMRDQEKLSLMYARKGVAEQKREKEIKSE LKMKQDAQVVLYRSYRHGDLPDIQIKHSSLITPLQAVAQRDPIIAKQLFSSLFSGILKEM DKFKTLSEKNNITQKLLQDFNRFLNTTFSFFPPFVSCIQDISCQHAALLSLDPAAVSAGC LASLQQPVGIRLLEEALLRLLPAELPAKRVRGKARLPPDVLRWVELAKLYRSIGEYDVLR GIFTSEIGTKQITQSALLAEARSDYSEAAKQYDEALNKQDWVDGEPTEAEKDFWELASLD CYNHLAEWKSLEYCSTASIDSENPPDLNKIWSEPFYQETYLPYMIRSKLKLLLQGEADQS LLTFIDKAMHGELQKAILELHYSQELSLLYLLQDDVDRAKYYIQNGIQSFMQNYSSIDVL LHQSRLTKLQSVQALTEIQEFISFISKQGNLSSQVPLKRLLNTWTNRYPDAKMDPMNIWD DIITNRCFFLSKIEEKLTPLPEDNSMNVDQDGDPSDRMEVQEQEEDISSLIRSCKFSMKM KMIDSARKQNNFSLAMKLLKELHKESKTRDDWLVSWVQSYCRLSHCRSRSQGCSEQVLTV LKTVSLLDENNVSSYLSKNILAFRDQNILLGTTYRIIANALSSEPACLAEIEEDKARRIL ELSGSSSEDSEKVIAGLYQRAFQHLSEAVQAAEEEAQPPSWSCGPAAGVIDAYMTLADFC DQQLRKEEENASVIDSAELQAYPALVVEKMLKALKLNSNEARLKFPRLLQIIERYPEETL SLMTKEISSVPCWQFISWISHMVALLDKDQAVAVQHSVEEITDNYPQAIVYPFIISSESY SFKDTSTGHKNKEFVARIKSKLDQGGVIQDFINALDQLSNPELLFKDWSNDVRAELAKTP VNKKNIEKMYERMYAALGDPKAPGLGAFRRKFIQTFGKEFDKHFGKGGSKLLRMKLSDFN DITNMLLLKMNKDSKPPGNLKECSPWMSDFKVEFLRNELEIPGQYDGRGKPLPEYHVRIA GFDERVTVMASLRRPKRIIIRGHDEREHPFLVKGGEDLRQDQRVEQLFQVMNGILAQDSA CSQRALQLRTYSVVPMTSRLGLIEWLENTVTLKDLLLNTMSQEEKAAYLSDPRAPPCEYK DWLTKMSGKHDVGAYMLMYKGANRTETVTSFRKRESKVPADLLKRAFVRMSTSPEAFLAL RSHFASSHALICISHWILGIGDRHLNNFMVAMETGGVIGIDFGHAFGSATQFLPVPELMP FRLTRQFINLMLPMKETGLMYSIMVHALRAFRSDPGLLTNTMDVFVKEPSFDWKNFEQKM LKKGGSWIQEINVAEKNWYPRQKICYAKRKLAGANPAVITCDELLLGHEKAPAFRDYVAV ARGSKDHNIRAQEPESGLSEETQVKCLMDQATDPNILGRTWEGWEPWM

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 2

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試料調製

結晶
IDマシュー密度 (Å3/Da)溶媒含有率 (%)解説
13.8668.15Author used the sf data from entry 5LUQ
23.8668.15Author used the sf data from entry 5LUQ
結晶化
温度 (K)Crystal-ID手法詳細
2931蒸気拡散法, ハンギングドロップ法0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 18% PEG 8000
2932蒸気拡散法, ハンギングドロップ法0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 8% PEG 8000

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データ収集

回折
ID平均測定温度 (K)Crystal-IDSerial crystal experiment
11001N
21002N
放射光源
由来サイトビームラインID波長 (Å)
シンクロトロンESRF ID2910.9791
シンクロトロンESRF ID23-120.9791
検出器
タイプID検出器日付
DECTRIS PILATUS 6M-F1PIXEL2012年5月23日
DECTRIS PILATUS 6M-F2PIXEL2011年6月25日
放射
IDプロトコル単色(M)・ラウエ(L)散乱光タイプWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
放射波長
ID波長 (Å)相対比
10.97911
21
反射解像度: 4.3→49.918 Å / Num. obs: 86508 / % possible obs: 97.8 % / 冗長度: 35.2 % / Biso Wilson estimate: 185.23 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 15.4
反射 シェル解像度: 4.3→4.4075 Å / Rmerge(I) obs: 0.936 / Num. unique obs: 0

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
PHENIX1.14_3260位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7K0Y

7k0y


解像度: 4.3→49.92 Å / SU ML: 0.7829 / 交差検証法: FREE R-VALUE / σ(F): 0 / 位相誤差: 41.5014 / 立体化学のターゲット値: CDL v1.2
Rfactor反射数%反射
Rfree0.3353 1978 2.34 %
Rwork0.2859 82547 -
obs0.287 84525 97.8 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 217.04 Å2
精密化ステップサイクル: LAST / 解像度: 4.3→49.92 Å
タンパク質核酸リガンド溶媒全体
原子数56895 0 0 0 56895
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00458016
X-RAY DIFFRACTIONf_angle_d0.861178589
X-RAY DIFFRACTIONf_chiral_restr0.04619116
X-RAY DIFFRACTIONf_plane_restr0.00549972
X-RAY DIFFRACTIONf_dihedral_angle_d21.596721262
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3-4.410.44281340.40485459X-RAY DIFFRACTION91.03
4.41-4.530.39251350.38385634X-RAY DIFFRACTION94.88
4.53-4.660.41961400.36355746X-RAY DIFFRACTION95.75
4.66-4.810.3931400.36755784X-RAY DIFFRACTION96.61
4.81-4.980.39371420.3655844X-RAY DIFFRACTION97.16
4.98-5.180.43291350.36055858X-RAY DIFFRACTION97.91
5.18-5.420.37051450.36755942X-RAY DIFFRACTION98.61
5.42-5.70.39361400.36925940X-RAY DIFFRACTION98.96
5.7-6.060.37251340.37546011X-RAY DIFFRACTION99.29
6.06-6.530.39621470.36725984X-RAY DIFFRACTION99.51
6.53-7.180.42381420.33356007X-RAY DIFFRACTION99.87
7.18-8.220.33221440.27236060X-RAY DIFFRACTION100
8.22-10.340.27071480.18776087X-RAY DIFFRACTION99.98
10.34-49.920.25331520.20956191X-RAY DIFFRACTION99.56
精密化 TLS手法: refined / Origin x: 21.7139499133 Å / Origin y: 21.6150386642 Å / Origin z: 73.977301847 Å
111213212223313233
T1.96910464944 Å20.23548057605 Å20.150643938936 Å2-1.29490198843 Å20.0785417600262 Å2--2.12038490571 Å2
L0.146615826474 °2-0.0775742632931 °2-0.0602368063791 °2-0.0467593383949 °20.0605389396786 °2--0.0563880726578 °2
S-0.118135563901 Å °-0.0474345978314 Å °0.00877954087073 Å °0.131806639157 Å °0.037162536322 Å °0.00270294463178 Å °-0.0434187020948 Å °0.0630773563929 Å °0.099795708351 Å °
精密化 TLSグループSelection details: all

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
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関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
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関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
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外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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